Harry Potter and Time's Children
by TimeWolfSaphira
Summary: Amy and Rory have gone, and the Doctor wants to retire. But the Tardis has other plans. Soon he's teaching at Hogwarts, has an inquisitive and curious 11 year old in tow who calls him "dad". Full summery inside.
1. Two Lonely Souls

**Full Summery: After losing Amy and Rory to the Weeping Angels, The Doctor decided to retire. The Tardis, however, had other plans for her thief. Now, he has a teaching position at 1991 Hogwarts, and has a energetic and inquisitive 11 year old girl in tow who calls him "dad". Will the Doctor be able to successful manage to teach a bunch of wizards and witches Muggle Studies, the proper and unbiased way? And will his 'daughter' and her friends stay out of trouble? And most importantly, will the Doctor accept his fate of being a father again? Or will he break both his hearts again by leaving her behind?**

**A/N: Grab a tissue box. This first chapter will contain lots of feels.**

**Chapter One**

**Two Lonely Souls**

Why? Why did that Angel take away his Amy and Rory? His beloved Ponds? His best friends? His- dare he say it- in-laws?

He had managed to save Amy and Rory from the Weeping Angels, save all of Manhattan. But one angel got through. One angel survived. And now he will forever hate that angel.

It had taken Rory first. They were on their way back to the Tardis, parked in the graveyard. Rory had called Amy's name, then he was gone. Just like that. In his place was a Weeping Angel, pointing its finger at the gravestone Rory had been staring at mere seconds ago. Engraved in the stone were the words:

_In Loving Memory_

_Rory Arthur Williams_

_Aged 82_

Amy, of course, was devastated. She asked, no _begged_ the Doctor to go back and save Rory. But it was impossible. Going back meant destroying all of New York. Even though he also wanted to save Rory, the Doctor knew he couldn't risk the hundreds of lives in the city. So instead of going on with the Doctor, she decided to join her husband.

And so the Angel had taken Amy from him.

And words were added to the gravestone:

_And his loving wife_

_Amelia Williams_

_Aged 87_

No longer will he trip over things the Ponds left lying around. No longer will he share adventures with his best friends. No more Amy. No more Rory. No more raggedy man.

No more Doctor.

He couldn't do this any longer. Both his hearts had been broken to many times. Now, they were shattered. And he doubted anyone could ever fix them.

Amy told River to stay with him. But she didn't. She left, and the Doctor knew the fate that awaited her. And that, too, broke his hearts.

_Victoria London, a nice place to retire_ the Doctor though to himself, messing around with the controls, but not with his usual energy. Madam Vastra, Jenny Flint, and Strax were there too. A least he'll have a little company.

The Tardis landed with a soft _thump_, but the Doctor stood at the controls awhile longer, fingering a lever. Sadness still overwhelmed him, and he couldn't bring himself to face his friends.

_Knock, knock, knock._

Well, now he didn't have a choice. They were probably wondering why he had turned up and not come out of the Tardis. So with a deep, yet shaky, breath, the Doctor composed himself and walked towards the door, opening it.

This was not Victoria London. This was 1991 London. And standing right outside his door was a little girl, must have been no older than 10 or 11, who looked so much like _her._ Same blonde hair, although a shade darker. Same nose, same mouth. But her eyes, _her eyes were wrong_. They weren't a dark brown, they were a bright blue. Blue like the Tardis.

"Hi dad."

The Doctor stared at the little girl blankly. _Dad?_ Did he hear her right? Did she just call him _dad?_ He hadn't been a father since... well, since Jenny. His Jenny. She only lived for barely a day, and Cobb had shot her. Well, he aimed at the Doctor, but Jenny shielded her father. Taken the bullet for him. And she barely had begun to live.

And now a little girl stood in front of him, calling him dad. A girl who looked so much like his Rose, it was painful. His pink and yellow human. The Doctor fell to his knees, leaning against the side of his Tardis. He was in shock.

A small hand brushed against his cheek, and he noticed that the little girl was wiping away his tears. _He was crying_. His green eyes gazed up at her big blue ones.

"Why are you crying?" she asked innocently. She wrapped her small, thin arms around his neck and sat down in his lap. The Doctor hesitated, then wrapped his own long arms around the tiny frame, burying his face into her hair and crying.

She had to be hers. She was a spitting image. But how did she get here? And where was Rose? No, he'll worry about that later. Right now he was holding onto something that connected him with his Rose.

"It's okay, Daddy," the little girl whispered, patting his head. "Mommy brought me here. She said to wait for you. Wait five and a half hours."

That sentence shot a stabbing pain through his hearts. _Wait five and a half hours,_ that's what he told Rose a long time ago. And now here was this little girl repeating those words he said all those years ago. He pulled away to look at the little girl in the face.

"Where is she now?" The Doctor asked, tears blurring his vision. The girl cocked her head.

"Went looking for Uncle Jack," she told him. "Said 'don't know how long it will take' and to give you lots of love." A pang of jealousy went through him, but he shoved it aside. Rose went to look for Jack because he was like a brother to her. And Rose wanted the Tardis family together.

"So you are Saphira's father?"

The Doctor looked up to see a stern looking, older woman in emerald green robes standing not to far away. Although her posture was that of a stern person, her face was soft from watching the reunion of father and daughter. _My daughter_.

"I suppose I am," the Doctor said shakily. "I'm the Doctor."

"Then you are her father," the older woman informed the Time Lord. "I am Professor Minerva McGonagall. Yes, I know that its all in the books- Miss Tyler informed me- however the books no longer exist; it is all reality. And your daughter is a witch."

"I get to learn magic!" his daughter, Saphira, exclaimed. Saphira, like the dragon from _Eragon._ Rose must have named her that because of her blue eyes. He hoped her to be as wise and beautiful as her dragon namesake.

"And we wish that you would teach Muggle Studies for a few years, so that you would be able to keep an eye on your daughter and teach her things she wouldn't learn from us," Minerva explained.

Him? Teach Muggle Studies? He did a teaching job once, and he ended up having to blow the school up to get rid of aliens. And now here was a witch whom he had read about in the _Harry Potter _books, asking him to teach. Teach magical children about the ordinary world. But was the world ordinary? One part of it was all magic and the other science. Well... there was always the possibility that he could help integrate the two worlds together. And he had Saphira, Rose, Jack, and possibly Minerva and Dumbledore helping. Saphira could help by converting the children (okay, that did not sound right. Much to Cyperman-ish). Rose would be his assistant teacher. Jack? Well he could work on the 'muggle' side of things.

"Please daddy?" Saphira begged, her big blue eyes staring imploringly up at him. Great Rassilon, Rose taught her the puppy look. The look that always seemed to win him over, even through he was over 9 centuries old (just _how_ old was he now?)

"Okay then," the Doctor agreed. "Call me Professor John Smith."

"Actually, we have told everyone that you are Professor _Evans_," Minerva corrected, peering down at the Time Lord. That was when the Doctor realized he was still sitting on the ground with Saphira in his lap. "John Smith is too obvious of a fake name, don't you agree?"

"So our family name is Evans? Saphira Evans, sounds like a beautiful name," the Doctor said, standing up. Saphira hopped off his lap, preening under the praise. "Rose Evans. Also beautiful. What shall my first name be, then?"

"You have a while to think of one. Tomorrow, I will take you both to Diagon Alley," Minerva said, leaving. "And Doctor," she called, "do take care of that family of yours. They are truly quite loyal to you." With that, the older woman left.

"So, do you want to go somewhere before we go Diagon Alley?" the Doctor asked, looking down at his daughter. He wanted to spend time getting to know the little girl before she was too occupied with school and friends. "Anywhere you'd like."

"Ooo, can we go to Disney World? Mum and I went there when the Vortex Manipulator accidentally overshot our destination and landed in Florida, summer, year 2006," Saphira replied. She was already starting to sound like a proper little Time Traveler already. "Oh, and can we take Harry with us? Mum gave me a background of Harry's past, and can we adopt him? I want a brother, and Harry would make an awesome brother. Oh, and I can't wait to meet Jack, he's going to pretend to be Mum's half-brother, so that's why I call him Uncle Jack, so that I don't make any slip-ups. Speaking of slip-ups, Mum told me about the time you both met Queen Victoria and saved her from a werewolf, and that she knighted both of you and banished you after wards! Ooo, do you think I'd get to meet a werewolf? Werewolves are awesome! So are dragons! I want to see a real dragon!"

"Blimey, you've got quite the gob," The Doctor interrupted when she paused to catch a breath.

"Yeah, Mum said that I get that from you," Saphira said, grinning cheekily. "So, can we take Harry with us to Disney? Oh, let's go in 2007, so that we don't run into Mum and I from the past."

"And how are we going to get Harry to come with us?" the Doctor asked. He wanted see how clever his daughter already was.

"We could kidnap him," she suggested. "Park the Tardis somewhere Harry runs when he's being chased by Mudley- I mean Dudley- and his friends, and he would run straight into it. Or so that it looks like a good hiding place. Park the Tardis on a corner, keep the door unlocked, and he'll use it as a hiding place. Or we could materialize the Tardis around him when he's with his relatives and give them a shock."

"Both of the first ideas sound good," the Doctor mused, "last one sounds brilliant, but we're not doing that."

"Nuts," Saphira huffed. "But we _are_ taking Harry along, right?"

"'Course we are," the Doctor replied, walking back into the Tardis. His daughter followed him, and gave an excited squeal.

"Oh, she's absolutely _beautiful!_" she said, turning to take in her surroundings. The Doctor smiled, and the Tardis gave a pleased hum that sounded oddly smug. He would have to ask Her about that later.

Amy and Rory were gone, but the Doctor would keep going, for them. His Rose was coming back, and so was Jack. It would be the old team again, before the Game Station happened. But this time, the would have a few additions to the team. He grinned down at his daughter, and she mirrored the smile as he set the Tardis in motion.

Maybe he should be thankful that the Tardis took him to his daughter, instead of Victorian London. Who knew how long he would last before he was traveling again?

**A/N: Don't worry, I'll be bringing Clara in at one point. She has started to grow on me. Hope you like the first chapter on my Doctor Who/Harry Potter crossover.**


	2. Kidnappings and Birthdays

**A/N: Took me a while to figure out a good kidnapping plan for the Doctor and Saphira. Then I got it. Hope you enjoy.**

**Chapter 2**

**Kidnappings and Birthdays**

A storm raged through the night; winds howling, rain pouring from the heavens above. Waves slapped against the small island that held only a run down hut.

Inside the hut, Harry Potter lay awake, listening to the sounds of the storm. His cousin, Dudley, was snoring way on the couch, while he, Harry, lay on the softest bit of ground with the thinnest blanket available covering him. He was lying on his stomach, finishing the drawing of a cake in the dirt. He glanced at the watch on Dudley's arm, which was dangling from the couch.

_12:00 am_

"Make a wish, Harry," he whispered to himself, as a gust of wind tugged at his hair. He blew out his imaginary candles. Just as he did, a strange groaning, wheezing sound filled the air.

_Vroop, vroop, vroop._

Harry glanced at the door and saw a very strange sight. A large blue box was appearing and disappearing; focusing and unfocusing. Harry watched the blue box land with a _thump!_ then glanced around in worry.

Dudley was still fast asleep, and no movement came from his Aunt and Uncle's room. He looked back at the box, and noticed that the door was ajar, a warm orange light falling onto him. Glancing around again, Harry got up and moved cautiously towards the box. When he was close to it, he reached out and placed a hand on the box. He immediately snatched his hand back when he felt that the wood was warm and humming. Harry gazed at the blue box that towered above him, then pushed the door and walked in.

He gaped when he saw the interior of the box. He back out again, and stared at the box; it was still a small box. Harry walked around the box; small and blue. He shook his head. He must be dreaming! There was no way that a box could be bigger on the inside than it was on the outside.

But there it was. The blue box that had a much bigger interior. Harry looked back to where his cousin slept, and towards the door, behind which his relatives slept. Coming to a decision, Harry walked back into the strange blue box, and closed the door behind him.

The room that he stepped into had a cozy, home-like feeling to it. It had a warm and soft orange glow; a large console sat at the center, a strange column at the center, going from floor to ceiling; there was a set of stairs that lead to a lower level; doorways indicating that there was more to the inside of the box; and strange bits and pieces he'd never seen before.

"Hello!"

Harry nearly jumped out of his skin when a man in a tweed jacket and floppy brown hair appeared from behind the console. He was grinning broadly.

"Welcome to the Tardis. My Tardis. That' S. Time and Relative Dimension in Space. This old girl can travel anywhere. Every star, every planet. Everything that ever happened or ever will. I'm the Doctor, and that there is my daughter, Saphira," the man- no Doctor, rambled, gesturing wildly with his hands, first at the whole interior of the box, then at himself, and finally at the girl behind him.

"I-I'm Harry. Harry Potter," Harry stammered. "Did you say this box can travel through time?"

"And space!" the girl, Saphira chipped in.

"Yes, and," the Doctor said, flipping a lever, "we're going to take you along. Hang on tight!"

Harry stumbled as the box- or Tardis as this Doctor called it- began to jerk and tremble. "What's happening?" he yelped, grabbing hold of the railing.

"We're traveling through time and space!" The Doctor laughed.

"Specifically, we are going to Disney World, Orlando, Florida, USA, North America, Northern Hemisphere, Earth, the Solar System!" Saphira chirped, clinging to the railing. "Summer of 2007!

The Tardis landed with a loud _thump_ and stilled. The Doctor pulled a monitor towards him, gazing at it. Harry cautiously let go of the railing, still a little shaky from the abrupt flight.

"So you basically kidnapped me from under my relatives' noses just to take me to Disney World?" Harry asked.

"Pretty much, yeah," Saphira nodded.

"Why me?"

"Cause you're very special, Harry Potter," the Doctor said, kneeling down to look the boy straight in his emerald green eyes. "And you missed a great deal of your childhood because of those so-called relatives."

"How do you know that?" Harry whispered.

"I'm a time-traveler. More to that, I am known as a Time Lord. The last one in existence. I can see all of time, and your time line shows me your past as well your possible futures. And we wanted to give you a childhood that you missed," the Doctor replied.

Harry felt heat rise up in his cheeks, and his heart felt lighter. Here was a man who traveled all of time and space, who could see it all, and he chose him, Harry Potter, to travel with. Not his cousin, _him._ He was special.

"Now, come on, we shouldn't waste such wonderful weather! We've got an amusement park to play in!" the Doctor exclaimed, jumping up.

"Hold on!" Saphira called, grabbing Harry's hand and dragging him through one doorway. "We've got to put on some better clothing! Mum told me about the Tardis' enormous wardrobe, so we're bound to find something more appropriate for you to put on!"

"Don't take to long! I know how you females like to take your time!" the Doctor called, getting a "yeah, yeah," and a dismissive wave from his daughter in reply.

"Do you know where this wardrobe is?" Harry asked, jogging to keep up with Saphira's fast pace.

"Nope!" She replied cheerfully. "But don't worry. The old girl will take us there."

Harry looked at the rounded corridors, and felt a tickle of reassurance at the back of his mind, as well as a soothing hum. He could hear the walls vibrate softly.

"Is this place alive?" he asked, a slight awe in his voice.

"Yep. Tardis are grown, not made. They are very powerful, sentential ships," Saphira replied. "Ah, here we go!" The duo walked into what reminded Harry of a clothing store and a costume store combined; there were so many different clothing from different time periods- past, present, and future. Harry gaped at the vastness of the place.

"Alright girl, what have you got for us?" Saphira asked, and an area lit up brighter then the rest, and Saphira immediately dragged Harry to that area.

It was filled with boy's clothing, and Saphira dug through the articles of clothing, examining them and putting them back when she didn't like it. Harry looked around himself, holding up different clothing, only for Saphira to make a face, which made him put it back. Eventually, Harry was shoved into a changing room with clothing that Saphira approved of, and had to try on different combinations.

Finally, they decided on a pair of loose fitting jeans, held up by a belt; a dark blue shirt with a gray wolf's head in front of a full moon; and some tennis shoes. Saphira had on matching clothing, but her shirt had a howling wolf on it. Both also had on red baseball caps on, and had slathered on lots of sunscreen to protect themselves from the sun.

"That way, in case we get lost, which hopefully won't happen, we know what to look for," Saphira explained as they walked back to the console room. The Doctor leapt up from where he was leaning against the console.

"You two took for ever!" he complained.

"Patience, dad," his daughter replied.

"Patience is for wimps!" he replied huffily, stomping out the door.

"No its not. Patience is a virtue!" Saphira called back, following her dad. Harry followed behind, a small grin on his face. The Doctor guided them towards the street and hailed a cabbie.

"You've got the correct currency? Saphira hissed to her dad as they climbed in.

"Don't worry, I got money while you two were changing," he replied in a low voice, then told the cabbie "take us to The Magical Kingdom of Disney World!"

-Line Break-

Harry grinned to himself as he curled up in his bed a week later. It was the best birthday he had ever had. They had not only visited Disney World, but also Universal Studios, and Bush Gardens. Harry now had a small collection of plushies, t-shirts, and other souvenirs.

The Tardis made him his own room, where he could keep all of his new things with out worrying about the Dursleys ever getting their hands on his things. He learned quickly how to communicate with the sentential ship; she 'spoke' through feelings, images, and different types of hums. He grew fond of the ship, and was happy that he was allowed to stay the rest of the summer on board.

Harry also learned about his magical heritage, as well as the truth of his parent's deaths. He couldn't wait to start his magic studies; and 'tomorrow' (there was no sense of time on the Tardis) they would meet with Professor McGonagall to get their school things.

Thinking back to the night when the Tardis appeared to him, he was pleased to have had the courage and curiosity to explore the blue box.

Only he did not know the danger that comes with being friends with the Time Lord.

**A/N: The next chapter will be on going to Diagon Alley. I'm debating on whether or not to bring in Hedwig, since Saphira and the Doctor will be 'kidnapping' Harry every summer. Maybe just as an animal companion. If so, I'll be turning the Master into a cat, and he'll be Koschei, Saphira's insane cat.**


End file.
